However, shopkeepers in the main markets in old city voluntarily observed the shutdown.
Police and paramilitary forces were deployed around Charminar and interior areas which witnessed communal clashes in November.
Asaduddin Owaisi described the arrest of his younger brother as a conspiracy by the Congress and the BJP.
He said he had full faith in the judiciary and hoped justice would be done in Akbar Owaisi's case.
A shutdown was observed in parts of Adilabad and Nizamabad districts on a call given by the MIM to protest the arrest.
MIM workers took our rallies in some places. The rally in Bodhan town of Nizamabad district led to tension.
Protestors also damaged media vehicles near a court in Nirmal.
Holding pictures of Akbar Owaisi and placards, the MIM activists also held a massive protest in Zaheerabad town in Medak district. They demanded immediate release of their leader.